Add more examples for black rhino project

examples/Gaasterland/README.mkdn

@@ -1,3 +1,5 @@
+This folder contains some examples of my work in the Gaasterland Lab.
+
 - [`delox.R.html`](delox.R.html): The R code
   for
   [Deloxer](https://academic.oup.com/nar/article/40/3/e24/1128321/Illumina-mate-paired-DNA-sequencing-library)
@@ -5,11 +7,6 @@
   consistency of coverage depth between 2 Exome sequencing replicates
 - [`illumina-qc.html`](illumina-qc.png): QC chart indicating quality
   score dropoff along read length for exome sequencing data set.
-- [`ipi-results-small.txt`](ipi-results-small.txt): A sample of output
-  showing alignment of *de novo* assembled black rhino and white rhino
-  transcript sequences to human proteins. This was used to find
-  differences between the two rhino species in otherwise conserved
-  regions.
 - [`mirna-results.html`](mirna-results.html): Example output from
   miRNA binding site predictions
 - [`neartarget.pdf`](neartarget.pdf): Visualization of mean coverage

examples/Gaasterland/index.html

@@ -1,9 +1,9 @@
+<p>This folder contains some examples of my work in the Gaasterland Lab.</p>
 <ul>
 <li><a href="delox.R.html"><code>delox.R.html</code></a>: The R code for <a href="https://academic.oup.com/nar/article/40/3/e24/1128321/Illumina-mate-paired-DNA-sequencing-library">Deloxer</a></li>
 <li><a href="depth-consistency.pdf"><code>depth-consistency.pdf</code></a>: Visualization of consistency of coverage depth between 2 Exome sequencing replicates</li>
 <li><a href="illumina-qc.png"><code>illumina-qc.html</code></a>: QC chart indicating quality score dropoff along read length for exome sequencing data set.</li>
-<li><a href="ipi-results-small.txt"><code>ipi-results-small.txt</code></a>: A sample of output showing alignment of <em>de novo</em> assembled black rhino and white rhino transcript sequences to human proteins. This was used to find differences between the two rhino species in otherwise conserved regions.</li>
 <li><a href="mirna-results.html"><code>mirna-results.html</code></a>: Example output from miRNA binding site predictions</li>
 <li><a href="neartarget.pdf"><code>neartarget.pdf</code></a>: Visualization of mean coverage depth in exome sequencing data in the regions flanking the probe targets.</li>
-<li><a href="on-off-coverage.pdf"><code>on-off-coverage.pdf</code></a>: Relationship between covered on-target bases and covered off-target bases in exome-seq data, with varying extensions of the target region to allow for &quot;near-target&quot; capture.</li>
+<li><a href="on-off-coverage.pdf"><code>on-off-coverage.pdf</code></a>: Relationship between covered on-target bases and covered off-target bases in exome-seq data, with varying extensions of the target region to allow for “near-target” capture.</li>
 </ul>

examples/Rhino/README.mkdn

@@ -0,0 +1,11 @@
+- [`ipi-results-small.txt`](ipi-results-small.txt): A sample of output
+  showing alignment of *de novo* assembled black rhino and white rhino
+  transcript sequences to human proteins. This was used to find
+  differences between the two rhino species in otherwise conserved
+  regions, using human as the phylogenetic outgroup.
+- [`rhino-abstract.pdf`](rhino-abstract.pdf) and
+  [`rhino-slides.pdf`](rhino-slides.pdf): Abstract and slides for a
+  talk incorporating my work on *de novo* assembly and mutation
+  analysis of the black rhino and white rhino transcriptomes,
+  presented at the 2013 International Elephant & Rhino Conservation &
+  Research Symposium

examples/Rhino/index.html

@@ -0,0 +1,4 @@
+<ul>
+<li><a href="ipi-results-small.txt"><code>ipi-results-small.txt</code></a>: A sample of output showing alignment of <em>de novo</em> assembled black rhino and white rhino transcript sequences to human proteins. This was used to find differences between the two rhino species in otherwise conserved regions, using human as the phylogenetic outgroup.</li>
+<li><a href="rhino-abstract.pdf"><code>rhino-abstract.pdf</code></a> and <a href="rhino-slides.pdf"><code>rhino-slides.pdf</code></a>: Abstract and slides for a talk incorporating my work on <em>de novo</em> assembly and mutation analysis of the black rhino and white rhino transcriptomes, presented at the 2013 International Elephant &amp; Rhino Conservation &amp; Research Symposium</li>
+</ul>

examples/Rhino/refs.bib

@@ -0,0 +1,78 @@
+
+@article{grabherrFulllengthTranscriptomeAssembly2011,
+  abstract = {Reconstructing full-length transcripts from high-throughput RNA sequencing data is difficult without a reference genome sequence. Grabherr et al. describe Trinity, an algorithm for assembling full-length transcripts from short reads without first mapping the reads to a genome sequence.},
+  author = {Grabherr, Manfred G. and Haas, Brian J. and Yassour, Moran and Levin, Joshua Z. and Thompson, Dawn A. and Amit, Ido and Adiconis, Xian and Fan, Lin and Raychowdhury, Raktima and Zeng, Qiandong and Chen, Zehua and Mauceli, Evan and Hacohen, Nir and Gnirke, Andreas and Rhind, Nicholas and di Palma, Federica and Birren, Bruce W. and Nusbaum, Chad and Lindblad-Toh, Kerstin and Friedman, Nir and Regev, Aviv},
+  date = {2011-07},
+  doi = {10/b2bctj},
+  file = {/Users/ryan/Documents/Zotero Library/Grabherr et al. - 2011 - Full-length transcriptome assembly from RNA-Seq da.pdf;/Users/ryan/Zotero/storage/IF5HC4CV/nbt.html},
+  issn = {1546-1696},
+  journaltitle = {Nature Biotechnology},
+  langid = {english},
+  number = {7},
+  pages = {644-652},
+  shortjournal = {Nat Biotechnol},
+  title = {Full-Length Transcriptome Assembly from {{RNA}}-{{Seq}} Data without a Reference Genome},
+  volume = {29}
+}
+
+@article{kumarPredictingEffectsCoding2009,
+  abstract = {The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5\textendash{}20 min, depending on the input. SIFT is available as an online tool (
+                  http://sift-dna.org
+                  
+                ).},
+  author = {Kumar, Prateek and Henikoff, Steven and Ng, Pauline C.},
+  date = {2009-07},
+  doi = {10/bk5p4w},
+  file = {/Users/ryan/Documents/Zotero Library/Kumar et al. - 2009 - Predicting the effects of coding non-synonymous va.pdf;/Users/ryan/Zotero/storage/JREYB9D9/nprot.2009.html},
+  issn = {1750-2799},
+  journaltitle = {Nature Protocols},
+  langid = {english},
+  number = {7},
+  pages = {1073-1081},
+  shortjournal = {Nat Protoc},
+  title = {Predicting the Effects of Coding Non-Synonymous Variants on Protein Function Using the {{SIFT}} Algorithm},
+  volume = {4}
+}
+
+@article{nemethRegulationIronMetabolism2006,
+  author = {Nemeth, Elizabeta and Ganz, Tomas},
+  date = {2006-08},
+  doi = {10/dggs8j},
+  file = {/Users/ryan/Zotero/storage/R4TE88ZN/Nemeth and Ganz - 2006 - Regulation of Iron Metabolism by Hepcidin.pdf},
+  issn = {0199-9885, 1545-4312},
+  journaltitle = {Annual Review of Nutrition},
+  langid = {english},
+  number = {1},
+  pages = {323-342},
+  shortjournal = {Annu. Rev. Nutr.},
+  title = {Regulation of {{Iron Metabolism}} by {{Hepcidin}}},
+  volume = {26}
+}
+
+@inproceedings{r.linzmeierRegulationIronBalance2008,
+  author = {{R. Linzmeier} and {M. Hakimi} and {E. Nemeth} and {T. Ganz} and {D. E. Paglia}},
+  booktitle = {Proc. {{Am}}. {{Assoc}}. {{Zoo Vet}}. {{Annu}}. {{Meet}}.},
+  date = {2008},
+  pages = {122-123},
+  title = {Regulation of Iron Balance in Four Species of Rhinoceroses}
+}
+
+@inproceedings{r.linzmeierRegulationIronBalance2013,
+  author = {{R. Linzmeier} and {R. Thompson} and {S. LaMere} and {P. Lee} and {D. E. Paglia} and {E. Nemeth} and {T. Ganz}},
+  booktitle = {Am. {{Assoc}}. {{Zoo Vet}}. {{Annu}}. {{Meet}}. ({{Abs}}. Submitted.)},
+  date = {2013},
+  title = {Regulation of Iron Balance in Rhinoceroses}
+}
+
+@article{SpecialSupplement2012,
+  date = {2012-09},
+  journaltitle = {Journal of Zoo and Wildlife Medicine},
+  langid = {english},
+  number = {3},
+  pages = {S1-S120},
+  shortjournal = {J. Zoo Wildl. Med.},
+  title = {Special {{Supplement}}},
+  volume = {43}
+}
+
+

examples/Rhino/rhino-abstract.lyx

@@ -0,0 +1,384 @@
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
+\lyxformat 544
+\begin_document
+\begin_header
+\save_transient_properties true
+\origin unavailable
+\textclass article
+\use_default_options true
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding auto
+\fontencoding global
+\font_roman "default" "default"
+\font_sans "default" "default"
+\font_typewriter "default" "default"
+\font_math "auto" "auto"
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100 100
+\font_tt_scale 100 100
+\use_microtype false
+\use_dash_ligatures true
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref true
+\pdf_bookmarks true
+\pdf_bookmarksnumbered false
+\pdf_bookmarksopen false
+\pdf_bookmarksopenlevel 1
+\pdf_breaklinks true
+\pdf_pdfborder true
+\pdf_colorlinks false
+\pdf_backref false
+\pdf_pdfusetitle true
+\papersize default
+\use_geometry false
+\use_package amsmath 1
+\use_package amssymb 1
+\use_package cancel 1
+\use_package esint 1
+\use_package mathdots 1
+\use_package mathtools 1
+\use_package mhchem 1
+\use_package stackrel 1
+\use_package stmaryrd 1
+\use_package undertilde 1
+\cite_engine biblatex
+\cite_engine_type numerical
+\biblio_options sorting=none
+\biblatex_bibstyle numeric
+\biblatex_citestyle numeric
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\justification true
+\use_refstyle 1
+\use_minted 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\is_math_indent 0
+\math_numbering_side default
+\quotes_style english
+\dynamic_quotes 0
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Title
+Current Studies on Molecular Mechanisms of Iron Homeostasis in Rhinoceroses
+\end_layout
+
+\begin_layout Author
+Rose Linzmeier, Ph.D.1
+\begin_inset Foot
+status collapsed
+
+\begin_layout Plain Layout
+Department of Pulmonary and Critical Care Medicine and Department of Pathology
+ and Laboratory Medicine, UCLA School of Medicine, Los Angeles, CA 90095
+\end_layout
+
+\end_inset
+
+ 
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+and
+\end_layout
+
+\end_inset
+
+ Ryan Thompson2
+\begin_inset Foot
+status collapsed
+
+\begin_layout Plain Layout
+Department of Molecular and Experimental Medicine, The Scripps Research
+ Institute, La Jolla, CA 92037
+\end_layout
+
+\end_inset
+
+ 
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+and
+\end_layout
+
+\end_inset
+
+ Sarah LaMere, D.V.M
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+footnotemark[2]
+\end_layout
+
+\end_inset
+
+ 
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+and
+\end_layout
+
+\end_inset
+
+ Pauline Lee, Ph.D.
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+footnotemark[2]
+\end_layout
+
+\end_inset
+
+ 
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+and
+\end_layout
+
+\end_inset
+
+ Elizabeta Nemeth, Ph.D.
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+footnotemark[1]
+\end_layout
+
+\end_inset
+
+ 
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+and
+\end_layout
+
+\end_inset
+
+ Tomas Ganz, M.D., Ph.D.
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+footnotemark[2]
+\end_layout
+
+\end_inset
+
+ 
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+and
+\end_layout
+
+\end_inset
+
+ Donald E.
+ Paglia, M.D.
+\begin_inset Foot
+status collapsed
+
+\begin_layout Plain Layout
+UCLA Hematology Research Laboratory, Department of Pathology and Laboratory
+ Medicine, UCLA School of Medicine, Los Angeles, CA 90095
+\end_layout
+
+\end_inset
+
+
+\begin_inset Note Note
+status collapsed
+
+\begin_layout Plain Layout
+Look into https://tex.stackexchange.com/q/34746/5654
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Date
+2013
+\end_layout
+
+\begin_layout Standard
+Iron storage disease (ISD) is a hazardous and clinically underappreciated
+ condition commonly acquired by exotic wildlife species when displaced from
+ their natural habitats and confined for even short periods under artificial
+ conditions.
+ An international symposium recently reviewed and validated evidence that
+ African black and Sumatran rhinoceroses invariably develop progressive
+ ISD commensurate with their times in captivity, whereas African white and
+ Indian rhinoceroses do not 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "SpecialSupplement2012"
+literal "false"
+
+\end_inset
+
+.
+ Since vulnerability to ISD is a species-wide characteristic, it is likely
+ to have a genetic basis possibly reflecting evolutionary adaptions to differenc
+es in iron bioavailability between browser and grazer diets.
+ 
+\end_layout
+
+\begin_layout Standard
+As a biologically essential element that is also highly toxic in excess,
+ iron is exquisitely regulated by molecular mechanisms primarily focused
+ on interactions between the peptide hepcidin, (the principal iron-regulatory
+ hormone), and its receptor ferroportin, (the sole channel for egress of
+ intracellular iron into plasma) 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "nemethRegulationIronMetabolism2006"
+literal "false"
+
+\end_inset
+
+.
+ Iron-regulatory gene sequences from both ISD-susceptible and non-susceptible
+ species were compared to search for possible molecular differences.
+ DNA was extracted from peripheral blood samples from all four available
+ rhinoceros species, and genes encoding hepcidin and ferroportin, as well
+ as modulators hemojuvelin, transferrin receptor 2, and HFE protein, were
+ cloned and analyzed by PCR amplification.
+ Over half of the DNA sequences of these five genes have now been determined
+ without identifying any that could account for disparities in iron loading
+ among the species.
+ Evaluation of the remaining sequences continues, as do studies to determine
+ the responsiveness of rhinoceros ferroportin to hepcidin modulation and
+ quantitative levels of hepcidin expression 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "r.linzmeierRegulationIronBalance2008"
+literal "false"
+
+\end_inset
+
+.
+ 
+\end_layout
+
+\begin_layout Standard
+In addition, liver and spleen mRNA sequences from African black and white
+ rhinoceroses were assembled using Trinity RNA-Seq software 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "grabherrFulllengthTranscriptomeAssembly2011"
+literal "false"
+
+\end_inset
+
+ and compared with human sequences using the SIFT algorithm 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "kumarPredictingEffectsCoding2009"
+literal "false"
+
+\end_inset
+
+.
+ Candidate single-nucleotide polymorphisms were independently validated
+ by genomic sequencing.
+ Mutations were found in four genes that may be associated with primary
+ iron disorders or hemolytic anemia in black rhinoceroses: SLC28a2, EPB41,
+ MTF1, and STEAP4 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "r.linzmeierRegulationIronBalance2013"
+literal "false"
+
+\end_inset
+
+.
+ The functional consequences of these mutations are being determined.
+\end_layout
+
+\begin_layout Standard
+\begin_inset CommandInset bibtex
+LatexCommand bibtex
+btprint "btPrintCited"
+bibfiles "refs"
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document

ryan_thompson_resume.lyx

@@ -1114,7 +1114,7 @@ Link:
 \begin_inset CommandInset href
 LatexCommand href
 name "Example results"
-target "https://darwinawardwinner.github.io/resume/examples/Gaasterland/ipi-results-small.txt"
+target "https://darwinawardwinner.github.io/resume/examples/Rhino/index.html"
 literal "false"
 
 \end_inset